You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 10 Next »

Information

Purpose: Molecular Dynamics
Latest version: 2.12
License: Mixed - Free for non-commercial users
Website: http://www.ks.uiuc.edu/Research/namd/ extlink-icon

NAMD is a molecular dynamics package.

NAMD implements standard MD capabilities (variety of integrators, thermostats, barostats, force field compatibility, PME electrostatics, timestep integration, replica exchange, free energy calculations, etc.).

 

 

SLURM Submit script example

For more information use the Job Script Generator.

namd_example.slm
#!/bin/bash
#SBATCH -J namd_example
#SBATCH -e namd_example.err
#SBATCH -o namd_example.out
#SBATCH -p std
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=4G

module load apps/namd/2.12

INPUT_DIR=${PWD}
OUTPUT_DIR=${PWD}

cd $SCRATCH
cp -r $INPUT_DIR/* $SCRATCH
namd2 +p4 namd_example.namd > namd_example.out
cp ./* $OUTPUT_DIR

 

Sbatch options:

  • -J: Specify a name for the job allocation. The default is the name of the batch script.
  • -e: Specify a name for the error output file.
  • -o: Specify a name for the output file.
  • -p: Specify the name of the partition (queue) where the job will be submited. The default is std.
  • --nodes: Number of nodes requested for allocation
  • --ntasks: Number of processes requested for allocation
  • --mem-per-cpu: Memory allocated per core.

 

 

  • No labels